| Install python and HTSeq Install perl Install R 2.15.3 (www.r-project.org). The installation of latest Bioconductor with all packages needed for the course is done run an R shell and writing the following code: source("http://bioconductor.org/biocLite.R") biocLite(c("Biobase", "limma", "affylmGUI", "tkWidgets", "GOstats", "AnnotationDbi", "preprocessCore", "IRanges", "baySeq", "Rsamtools", "R.utils", "annotate", "genefilter", "maSigPro", "pamr", "pdmclass", "ChIPpeakAnno", "chipseq", "BSgenome", "Rgraphviz", "affy" ,"annaffy", "affyPLM", "multtest", "ssize", "sizepower", "siggenes", "RankProd", "org.Hs.eg.db", "org.Mm.eg.db", "org.Rn.eg.db", "edgeR", "metaArray", "MergeMaid", "biomaRt", "GenomeGraphs","AffyCompatible", "Biostrings", "rtracklayer", "Genominator", "hugene10sttranscriptcluster.db", "mogene10sttranscriptcluster.db", "ragene10sttranscriptcluster.db", "HuExExonProbesetLocation", "MoExExonProbesetLocation", "RaExExonProbesetLocation", "snow", "RmiR", "RmiR.Hs.miRNA", "R.utils", "EDASeq","DESeq", "DEXSeq","goseq", "BSgenome.Hsapiens.UCSC.hg19", "TxDb.Hsapiens.UCSC.hg19.knownGene", "oneChannelGUI","chimera", "cummeRbund")) When installation is finished. You can load the library(oneChannelGUI). To start oneChannelGUI follow the instruction given int the first set of course slides or in the oneChannelGUI user guide. All NGS tools external to Bioconductor can be installed using oneChannelGUI functionalities, please read the vignettes. In order to use MIDAS from APT tools for exon array analysis the APT tool version 1.12.0 has to be used: http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx?hightlight=true&rootCategoryId=34002#1_3 This because MIDAS was not included in subsequent version since it was not changed. Windows users: For the correct installation of Rgraphviz , a library used for GO network visualization it is necessary: Go to: http://www.stats.ox.ac.uk/~ripley/Win64/W64porting.html , which has a link to a 64-bit abridged version of graphviz which has been built for 64-bit windows. 1. Extracted the archive (http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/) to a folder, eg. C:\graphviz64\graphviz 2. Changed PATH environment variable to point to new location of graphviz 3. used source("http://bioconductor.org/biocLite.R") biocLite("Rgraphviz") to install the 64-bit binary 4. Restart R |
| ADDITIONAL INFORMATION |
| Affymetrix
test data sets and exercises |
| oneChannelGUI
tutorial and exercises 1st part |
| oneChannelGUI tutorial and exercises 2nd part |
| Set of data to test the functionalities of
oneChannelGUI |
| 3IVT
two class unpaired test set to test oneChannelGUI
statistical tests, filtering, etc. |
| Data set derved from processed data file from E-TABM-158 ArrayExpress data set to test oneChannelGUI classification modules |
| Two GEO data sets to test oneChannelGUI statistical tests, filtering, etc. |
| Tab delimited file data set, based on moe4302, to test oneChannelGUI statistical tests, filtering, etc |
| Time
course data set to test maSigPro implementation of
oneChannelGUI |
| Hs/Mm/Rat
two
class unpaired data sets to test oneChannelGUI exon
modules |